s = calloc(c->l_qseq, 1);
for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
r = calloc(xe - xb, 1);
- for (i = xb; i < xe; ++i)
+ for (i = xb; i < xe; ++i) {
+ if (ref[i] == 0) { xe = i; break; }
r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
+ }
state = calloc(c->l_qseq, sizeof(int));
q = calloc(c->l_qseq, 1);
kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
fprintf(stderr, " -b compressed BAM output\n");
fprintf(stderr, " -S the input is SAM with header\n");
fprintf(stderr, " -A modify the quality string\n");
- fprintf(stderr, " -r read-independent local realignment\n\n");
+ fprintf(stderr, " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n");
+ fprintf(stderr, " -E extended BAQ for better sensitivity but lower specificity\n\n");
return 1;
}
fp = samopen(argv[optind], mode_r, 0);